The Model doesn't appear when rendering....? UPDATE
I believe it is because you are using the multiply node in the compositor. The multiply node is kind of like mixing two things in a way so that the brightness value is the factor (sorry if this doesn't make sense, there are lots of better explanations out on the internet). When you multiply the Suzanne and the movie clip, since the suzanne is white, it doesn't show through. 

I made a few changes to your composite setup. First I checked the Object Index pass under the Render Layers tab. I assigned Suzanne a pass index of 1 and the ground a pass index of 2. I wasn't able to get a good picture so I'm attaching a link to the .blend file but essentially, I masked out everything but the Suzanne and then used the mask to mix the head back in if that makes sense. Here's what the render looked like. Of course you would replace the color grid with your video.





Hope this helps! Good luck!